T cell immune recognition and clearance of pathogen-infected cells relies on the presentation of pathogen-derived peptides by MHC molecules. These peptides come from the degradation of pathogen-derived antigens by the antigen processing machinery of cellular compartments in which the pathogen enters and replicates. In chronic infections such as HIV or MTb the degradation processes and nature of peptides presentable by cells during infection or latency reversal are neither well defined nor predictable despite their critical role for immune recognition. The Le Gall laboratory studies the mechanisms of protein degradation, epitope processing and presentation to immune cells in the context of HIV, CMV, MTb infections or vaccination using adenovirus- or CMV-based vectors. Using a combination of biochemical, mass spectrometry approaches and computational analyses we define the proteome and peptidome of infected cells, explore the links between degradation patterns of antigens and immunogenicity in natural infection, define sequence signatures associated with peptide processing efficiency. Our goal is to identify and eventually predict pathogen-derived targets and decoys processed and displayed by cells during infection that will inform vaccine immunogen design and also identify novel mechanisms of immune escape.